A temporally stratified extension of space-for-time Cormack-Jolly-Seber for migratory animals.

Understanding drivers of temporal variation in demographic parameters is a central goal of mark-recapture analysis. To estimate the survival of migrating animal populations in migration corridors, space-for-time mark-recapture models employ discrete sampling locations in space to monitor marked populations as they move past monitoring sites, rather than the standard practice of using fixed sampling points in time. Because these models focus on estimating survival over discrete spatial segments, model parameters are implicitly integrated over the temporal dimension. Furthermore, modeling the effect of time-varying covariates on model parameters is complicated by unknown passage times for individuals that are not detected at monitoring sites. To overcome these limitations, we extended the Cormack-Jolly-Seber (CJS) framework to estimate temporally stratified survival and capture probabilities by including a discretized arrival time process in a Bayesian framework. We allow for flexibility in the model form by including temporally stratified covariates and hierarchical structures. In addition, we provide tools for assessing model fit and comparing among alternative structural models for the parameters. We demonstrate our framework by fitting three competing models to estimate daily survival, capture, and arrival probabilities at four hydroelectric dams for over 200 000 individually tagged migratory juvenile salmon released into the Snake River, USA.

A dynamic-bioenergetics model to assess depth selection and reproductive growth by lake trout (Salvelinus namaycush).

We coupled dynamic optimization and bioenergetics models to assess the assumption that lake trout (Salvelinus namaycush) depth distribution is structured by temperature, food availability, and predation risk to maximize reproductive mass by autumn spawning. Because the model uses empirical daily thermal-depth profiles recorded in a small boreal shield lake (lake 373 at the Experimental Lakes Area, northwestern Ontario) during 2 years of contrasting thermal stratification patterns, we also assessed how climate-mediated changes in lakes may affect the vertical distribution, growth, and fitness of lake trout, a cold-water top predator. The depths of acoustic-tagged lake trout were recorded concurrently with thermal-depth profiles and were compared to model output, enabling an assessment of model performance in relation to the observed fish behavior and contrasting thermal conditions. The depths and temperatures occupied by simulated fish most closely resembled those of the tagged fish when risk of predation was included in the model, indicating the model may incorporate the most important underlying mechanisms that determine lake trout depth. Annual differences suggest less use of shallow (warm), productive habitats, resulting in markedly less reproductive mass, during the year with the warm stratification pattern. Mass for reproduction may be lower in warmer conditions because of reduced reproductive investment, yet survival may be inadvertently higher because risky surface waters may be avoided more often in warmer, shallower, and metabolically costly conditions. At a minimum our study suggests that lake trout reproductive mass and fitness may be expected to change under the anticipated longer and warmer stratification patterns.

Movement and behavioral states of common carp (Cyprinus carpio) in response to a behavioral deterrent in a navigational lock.

BACKGROUND: Freshwater ecosystems are some of the most affected by biological invasions due, in part, to the introduction of invasive carp worldwide. Where carp have become established, management programs often seek to limit further range expansion into new areas by reducing their movement through interconnected rivers and waterways. Lock and dams are important locations for non-physical deterrents, such as carbon dioxide (CO2), to reduce unwanted fish passage without disrupting human use. The purpose of this study was to evaluate the behavioral responses of common carp (Cyprinus carpio) to non-physical deterrents within a navigation structure on the Fox River, Wisconsin. Acoustic telemetry combined with hidden Markov models (HMMs) was used to analyze variation in carp responses to treatments. Outcomes may inform CO2 effectiveness at preventing invasive carp movement through movement pinch-points. METHODS: Carbon dioxide (CO2) was recently registered as a pesticide in the United States for use as a deterrent to invasive carp movement. As a part of a multi-component study to test a large-scale CO2 delivery system within a navigation lock, we characterized the influence of elevated CO2 and forced water circulation in the lock chamber on carp movements and behavior. Through time-to-event analyses, we described the responses of acoustic-tagged carp to experimental treatments including (1) CO2 injection in water with forced water circulation, (2) forced water circulation without CO2 and (3) no forced water circulation or CO2. We then used hidden Markov models (HMMs) to define fine-scale carp movement and evaluate the relationships between carp behavioral states and CO2 concentration, forced water circulation, and temperature. RESULTS: Forced water circulation with and without CO2 injection were effective at expelling carp from the lock chamber relative to null treatments where no stimulus was applied. A portion of carp exposed to forced water circulation with CO2 transitioned from an exploratory to an encamped behavioral state with shorter step-lengths and a unimodal distribution in turning angles, resulting in some carp remaining in the lock chamber. Whereas carp exposed to forced water circulation only remained primarily in an exploratory behavioral state, resulting in all carp exiting the lock chamber. CONCLUSION: Our findings illustrate the potential of forced water circulation, alone, as a non-physical deterrent and the efficacy of CO2 injection with forced water circulation in expelling carp from a navigation lock. Results demonstrate how acoustic telemetry and HMMs in an experimental context can describe fish behavior and inform management strategies.

A bioenergetics evaluation of temperature-dependent selection for the spawning phenology by Snake River fall Chinook salmon.

High water temperatures can increase the energetic cost for salmon to migrate and spawn, which can be important for Snake River fall-run Chinook salmon because they migrate great distances (>500 km) at a time when river temperatures (18-24°C) can be above their optimum temperatures (16.5°C). Average river temperatures and random combinations of migration and spawning dates were used to simulate fish travel times and determine the energetic consequences of different thermal experiences during migration. An energy threshold criterion (4 kJ/g) was also imposed on survival and spawning success, which was used to determine how prevailing temperatures might select against certain migration dates and thermal experiences, and in turn, explain the selection for the current spawning phenology of the population. Scenarios of tributary use for thermal refugia under increasing water temperatures (1, 2, and 3°C) were also run to determine which combinations of migration dates, travel rates, and resulting thermal experiences might be most affected by energy exhaustion. As expected, when compared to observations, the model under existing conditions and energy use could explain the onset, but not the end of the observed spawning migration. Simulations of early migrants had greater energy loss than late migrants regardless of the river temperature scenario, but higher temperatures disproportionately selected against a larger fraction of early-migrating fish, although using cold-water tributaries during migration provided a buffer against higher energy use at higher temperatures. The fraction of simulated fish that exceeded the threshold for migration success increased from 58% to 72% as average seasonal river temperatures over baseline temperatures increased. The model supports the conclusion that increases in average seasonal river temperatures as little as 1°C could impose greater thermal constraints on the fish, select against early migrants, and in turn, truncate the onset of the current spawning migration.

Long-term comparisons between two-way satellite and geodetic time transfer systems.

Global Positioning System (GPS) observations recorded in the United States and Europe were used to evaluate time transfer capabilities of GETT (geodetic time transfer). Timing estimates were compared with two-way satellite time and frequency transfer (TWSTFT) systems. A comparison of calibrated links at the U.S. Naval Observatory, Washington, D.C., and Colorado Springs, CO, yielded agreement of 2.17 ns over 6 months with a standard deviation of 0.73 ns. An uncalibrated link between the National Institute of Standards and Technology (NIST) and Physikalisch-Technische Bundesanstalt, Braunschweig, Germany, has a standard deviation of 0.79 ns over the same time period.

Absolute calibration of a geodetic time transfer system.

An absolute calibration technique is developed for geodetic Global Positioning System (GPS) receivers. An uncertainty budget for the system (receiver, cables, connectors, antenna) is evaluated, yielding 1.1 ns at each frequency, and 1.6 ns for a two-receiver experiment. Analysis of data on a short baseline yields 0.8 and 1.2 ns agreement on P1 and P2, respectively.

Characterization of Isolates of Streptococcus agalactiae from Diseased Farmed and Wild Marine Fish from the U.S. Gulf Coast, Latin America, and Thailand.

We examined Lancefield serogroup B Streptococcus isolates recovered from diseased, cultured hybrid Striped Bass (Striped Bass Morone saxatilis × White Bass M. chrysops) and wild and cultured Gulf Killifish Fundulus grandis from coastal waters of the U.S. Gulf of Mexico (Gulf coast) and compared those isolates to strains from tilapias Oreochromis spp. reared in Mississippi, Thailand, Ecuador, and Honduras and to the original Gulf coast strain identified by Plumb et al. ( 1974 ). The isolates were subjected to phylogenetic, biochemical, and antibiotic susceptibility analyses. Genetic analysis was performed using partial sequence comparison of (1) the 16S ribosomal RNA (rRNA) gene; (2) the sipA gene, which encodes a surface immunogenic protein; (3) the cspA gene, which encodes a cell surface-associated protein; and (4) the secY gene, which encodes components of a general protein secretion pathway. Phylogenies inferred from sipA, secY, and cspA gene sequence comparisons were more discriminating than that inferred from the 16S rRNA gene sequence comparison. The U.S. Gulf coast strains showed a high degree of similarity to strains from South America and Central America and belonged to a unique group that can be distinguished from other group B streptococci. In agreement with the molecular findings, biochemical and antimicrobial resistance analyses demonstrated that the isolates recovered from the U.S. Gulf coast and Latin America were more similar to each other than to isolates from Thailand. Three laboratory challenge methods for inducing streptococcosis in Gulf Killifish were evaluated-intraperitoneal (IP) injection, immersion (IMM), and immersion plus abrasion (IMMA)-using serial dilutions of S. agalactiae isolate LADL 97-151, a representative U.S. Gulf coast strain. The dose that was lethal to 50% of test fish by 14 d postchallenge was approximately 2 CFU/fish via IP injection. In contrast, the fish that were challenged via IMM or IMMA presented cumulative mortality less than 40% by 14 d postchallenge.